My view is that while sanctions do have an oppressive nature (regardless if they are performed as part of the socialization of individuals or as part of the attempt to force nations to conform to international norms), they can be justified in many cases and may be applied if perceived as effective towards achieving moral goals.
I will refer to three types of sanctions that are typically discussed: Sanctions against Jewish settlements in the occupied territories, sanctions against the state of Israel, and sanctions against Israeli academic institutes.
In both cases, exercising sanctions is an act of violence (i.e., it is an act aimed at enforcing something on somebody against his/her will), where the violence may be symbolic or real. In both cases, the justification is that the norms that need to be enforced are more important than the violation of the target's individuality involved in applying force on him/her.
The social norms (or socially desirable behaviors) are not necessarily good or moral. But if we disapprove of the norms and/or of their binding power, then we should criticize the norms and/or their power, not the fact that sanctions may be applied in order to enforce them. In other words, a principled (rather than practical) objection to (resp., support of) certain sanctions must rely on a principled objection to (resp., support of) the goals that the sanctions are aimed at achieving.
Since the essence of the settlements is a harsh violation of these norms and since it necessitates a host of oppressive actions that violate the human rights of the Palestinians, sanctions against it are not only allowed but rather required. I wish to stress that the essence of the project and what it necessarily causes are the basis for a categorical opposition to it. This stands in contrast to a project that may have negative potentials that may be materialized but are not bound to materialize. The above distinction brings up to the next issue.
Still, the fact that Israel is currently involved in extreme and systematic violations of the international norms (w.r.t its actions in the occupied Palestinian territories), suggests that sanctions against it can be justified. As discussed below, the fact that sanctions can be justified does not mean that they must be applied.
But before discussing the latter issue, I wish to address a couple of arguments that are often raised against such sanctions. The first is that one should not mix science with politics, and the second is that it is unfair to harm Israeli academics (who may also disapprove of Israel's actions in the occupied territories).
Answering ``One should not mix science with politics.'' Without entering an argument regarding the question of whether science is actually separated from politics (and whether such a separation is at all possible), I wish to object to the categorical statement made above. Obviously, one can envision circumstances in which an academic boycott on a state is justified (e.g., in the case of the NAZI state). Note that I'm not saying that these circumstances exist in the case of Israel (nor that it reached the evils of the NAZI state), but rather that one should not make such categorical statements.
A detour: It is interesting that the ``call for purity'' (i.e., ``do not mix science with politics''), which is also raised w.r.t culture, is not raised w.r.t commerce. Why is this? One answer may be that everybody knows that commerce (and all economic activities) is impure in nature (i.e., it has no claim to being pure of circumstances). Another answer may be that, although the economic ideology demands independence from politics, economy actually relies on politics and is mixed in it. My own answer is different: It is that, at the current era, economy claims dominance on all spheres of life and they deny any attempted autonomy of any other sphere. Hence, the economic ideology views the proponents of sanctions as irrational (i.e., as failing to act according to the rational of markets), and has no way of debating with them (or with anybody who does not accept the economic axioms).
Answering ``unfair to harm Israeli academics.'' It seems a fact that opposition to the continued occupation of the Palestinian territories and the oppression involved in it is greater among academics (in Israel than in the general Jewish public in Israel). However, this opposition is individualized, and the Israeli academia as a body never took a stand on this political issue. Hence, some individuals may raise a claim of fairness, but the Israeli academia as a body cannot raise this claim. Furthermore, every sanction (e.g., a workers strike) may cause harm to some neutral and/or innocent parties; hence, such a claim of fairness is bound to oppose almost all public sanctions.
Let me comment that although the Israeli academia does collaborate with the Israeli occupation of the Palestinian territories and with the Jewish settlements in them (mostly indirectly), it is unfair to portray it as a spearhead of that project. Nor is it a spearhead of the objection to this project. Hence, in my opinion, the question of justification of sanctions on the Israeli academia reduces to the question of their effectiveness towards stopping the Israeli occupation of the Palestinian territories.
While I think that a comprehensive set of economical sanctions on Israel may have the desired effect, I doubt very much that something positive can be achieved by academic sanctions that remain confined to academic targets. Hence, unless the goal of academic sanctions is to spearhead a wide movement of comprehensive economical sanctions, academic sanctions on Israel are quite futile. The latter claim is related to the weak standing of academia in the Israel public, which is an adequate subject for a separate essay.
I refuse in principle to express an opinion (or even form an opinion) regarding whether sanctions on Israel and/or on Israeli academia are a good idea at this point. The reason is two-fold: Firstly, it is not for me to decide what others should do nor advise them on their actions, unless I see a moral imperative (whereas, as stated above, I see no moral imperative here). Secondly, it feels even more inadequate to advise others on actions that may effect me, while pretending that I have no stake. Of course, I do not want to be boycotted, but this is almost a tautology.